MDTools

Набор MDTools - коллекция программ, подлинников, и утилит от Theoretical and computational biophysics group для исследователей, чтобы обглечить выполнение различных задач по моделированию.
Каждый инструмент, подлинник, или библиотека упомянуты ниже.
Программы в этой коллекции обеспечены в пользу научного сообщества, но официально не поддержаны, если иначе не заявлено.
У каждой программы могут быть лицензия на программное обеспечение .

Работа над всеми проектами, по крайней мере, частично финансируется НNational Institutes of Health (grant number PHS 5 P41 RR05969).

CatDCD - Concatenates DCD multiple trajectory files, can select subset of atoms, think of Unix "cat".
Chemical2vmd - Lets VMD act as a helper application for chemical/x-vmd MIME type in web browsers
Conect2psf - Converts PDB "CONECT" records into a "PSF" file for proper bond display in VMD
FlipDCD/FixDCD - DCD trajectory file endianism and header conversion
Ionize - Parallelized ion placement tool
JMV: Java Molecular Viewer - JMV is a molecular viewer written in Java and Java3D. JMV is designed to be an easy-to-use platform neutral molecular visualization tool, which can be used standalone or integrated into other programs.
MDAPI - Application programming interface for molecular dynamics simulation engines
MDEnergy - Calculate energies from DCD or PDB files
MDTools for Python - Protein structure and dynamics analysis classes
MDX - Collection of C libraries to enable development of methods for molecular dynamics of biomolecules
MatDCD - A Matlab package for reading and writing DCD format trajectory files
Mindy - A "minimal" molecular dynamics program based on the NAMD source code
Mol_Volume - A program for calculating macromolecular volume
PDBCat - A tool for PDB file text processing and conversion
SODIUM - Arrange ions around biological macromolecules
volutil - manipuate 3D volumetric data in VMD
Wat2ions - Places ions in a water bath. A companion program to Delphi.
Web Database Application Framework
DBIx::Frame - An extension of Perl DBI which a framework with better logging, and standardized interfaces to common operations. The basic framework for the below databases.
TCB::Publications - a publications database.
TCB::Seminar - a seminar database.
TCB::System - A sysadmin database, based on DBIx::Frame. Uses the following sub-packages:
TCB::Equipment - Equipment and Software
TCB::Loan - Equipment Loans
TCB::Help - Help Database
TCB::SysLoads - System Loads and Supercomputers
TCB::PortMap - Port Map
TCB::System::Obsolete - Obsolete Tables
TCB::Conference - a conference registration database.
TCB::Library - a library book database.
TCB::AddressBook - a basic address book.
TCB::mysql - interface to the mysql authorization database.
Web, Programming, and Administrative Tools
TCB Script Library - small scripts that are too small to package separately, but may still be useful to many people.
TapeChanger::MTX - Perl module to control tape changers, using the MTX package.
TCB::Backup - perl scripts for performing our backups.
TCB::RSS - code to manage RSS feeds and lists of updated web pages.
Mail::SpamAssassin::UIUC - use the campus spam filtering service with SpamAssassin
TCB::Internal - Perl module for performing TCB web page layouts
TCB::AddUser - Perl module for adding and managing users
CGI::SHTML - Perl module for parsing Server-Side Includes.
TCB::Webdav - mount webdav partitions on Linux boxes, specifically BioCoRE and Netfiles.
HTML::FormRemove - Perl module for removing form tags from HTML.
make_tn - a script used to create thumbnail images and a web page to index them
Projector - RS-232 control/automation software for Electrohome Marquee series CRT projectors
SoftDB - A web-based, medium scale, field-specific software database
Sysload - Machine load monitoring system for clusters, departments
Usagemon - Software usage/event tracking system
Swing Test - Java Swing Detection Applet for Web Browsers

Со всеми этими программами и утилитами можно ознакомиться и скачать здесь:

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